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<meta name="author" content="Chen Tong" />
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Overview of BIC</a></li>
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<li class="chapter" data-level="1.1" data-path="data-transform.html"><a href="data-transform.html#introduction-of-the-common-data"><i class="fa fa-check"></i><b>1.1</b> Introduction of the common data</a>
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<li class="chapter" data-level="1.1.1" data-path="data-transform.html"><a href="data-transform.html#wide-matrix"><i class="fa fa-check"></i><b>1.1.1</b> Wide Matrix</a></li>
<li class="chapter" data-level="1.1.2" data-path="data-transform.html"><a href="data-transform.html#long-matrix"><i class="fa fa-check"></i><b>1.1.2</b> Long Matrix</a></li>
<li class="chapter" data-level="1.1.3" data-path="data-transform.html"><a href="data-transform.html#fasta"><i class="fa fa-check"></i><b>1.1.3</b> FASTA</a></li>
<li class="chapter" data-level="1.1.4" data-path="data-transform.html"><a href="data-transform.html#fastq"><i class="fa fa-check"></i><b>1.1.4</b> FASTQ</a></li>
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<li class="chapter" data-level="1.2" data-path="data-transform.html"><a href="data-transform.html#long-to-wide-matrix"><i class="fa fa-check"></i><b>1.2</b> Long To Wide Matrix</a></li>
<li class="chapter" data-level="1.3" data-path="data-transform.html"><a href="data-transform.html#merge-matrixes"><i class="fa fa-check"></i><b>1.3</b> Merge matrixes</a></li>
<li class="chapter" data-level="1.4" data-path="data-transform.html"><a href="data-transform.html#wide-to-long-matrix"><i class="fa fa-check"></i><b>1.4</b> Wide To Long Matrix</a></li>
<li class="chapter" data-level="1.5" data-path="data-transform.html"><a href="data-transform.html#reverse-complement-sequences"><i class="fa fa-check"></i><b>1.5</b> Reverse Complement Sequences</a></li>
<li class="chapter" data-level="1.6" data-path="data-transform.html"><a href="data-transform.html#rna-translation"><i class="fa fa-check"></i><b>1.6</b> RNA translation</a></li>
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<li class="chapter" data-level="2.7" data-path="plot.html"><a href="plot.html#enrichment-plot"><i class="fa fa-check"></i><b>2.7</b> Enrichment plot</a></li>
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<li class="chapter" data-level="2.9" data-path="plot.html"><a href="plot.html#scatter-plot"><i class="fa fa-check"></i><b>2.9</b> Scatter plot</a></li>
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<li class="chapter" data-level="2.12" data-path="plot.html"><a href="plot.html#eulerdiagrams-plot"><i class="fa fa-check"></i><b>2.12</b> EulerDiagrams plot</a></li>
<li class="chapter" data-level="2.13" data-path="plot.html"><a href="plot.html#non-classical-venn"><i class="fa fa-check"></i><b>2.13</b> Non-classical venn</a></li>
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<div id="data-transform" class="section level1 hasAnchor" number="1">
<h1><span class="header-section-number">1</span> Data<a href="data-transform.html#data-transform" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="introduction-of-the-common-data" class="section level2 hasAnchor" number="1.1">
<h2><span class="header-section-number">1.1</span> Introduction of the common data<a href="data-transform.html#introduction-of-the-common-data" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<div id="wide-matrix" class="section level3 hasAnchor" number="1.1.1">
<h3><span class="header-section-number">1.1.1</span> Wide Matrix<a href="data-transform.html#wide-matrix" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>Each column in Wide format is a variable, which is more like common gene expression data. For example, each row is a gene, and each column is a sample. It is suitable for a regular matrix and has good readability.</p>
</div>
<div id="long-matrix" class="section level3 hasAnchor" number="1.1.2">
<h3><span class="header-section-number">1.1.2</span> Long Matrix<a href="data-transform.html#long-matrix" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>The simplest format of Long format is two columns, one column contains all variable types, as in the sample mentioned earlier, one column contains all values. The common gene expression matrix is converted from Wide format to Long format and has three columns, one column is GeneID, one column is sample name, and the other column (usually column name is value) is the gene expression value, which represents the expression level of the corresponding gene in the corresponding sample. This format is convenient for program processing and is also suitable for irregular data.</p>
</div>
<div id="fasta" class="section level3 hasAnchor" number="1.1.3">
<h3><span class="header-section-number">1.1.3</span> FASTA<a href="data-transform.html#fasta" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>he FASTA format was developed as a text-based format to represent nucleotide or protein sequences.
An example fasta file showing the first part of the PAX6 gene.</p>
<pre><code>&gt;NG 008679.1:5001-38170 Homo sapiens paired box 6 (PAX6)
ACCCICTTTICITAICATIGACATTIAAACTCIGGGGCAGGICCICGCGIAGAACGCGGCIGTCAGATCI
GCCACTICCCCIGCCGAGCGGCGGTGAGAAGTGTGGGAACCGGCGCIGCCAGGCTCACCIGCCICCCCGC
CCICCGCTCCCAGGTAACCGCCCGGGCICCGGCCCCGGCCCGGCTCGGGGCCCGCGGGGCCTCICCGCIG
CCAGCGACTGCTGTCCCCAAATCAAAGCCCGCCCCAAGTGGCCCCGGGGCTIGATTTITGCTTTTAAAAG
GAGGCATACAAAGATGGAAGCGAGTTACTGAGGGAGGGATAGGAAGGGGGGTGGAGGAGGGACTTGTCIT
IGCCGAGTGTGCICIICIGCAAAAGTAGCAAAATGTICCACICCTAAGAGTGGACTICCAGTCCGGCCCT
GAGCIGGGAGTAGGGGGCGGGAGTCIGCTGCTGCIGICTGCTAAAGCCACTCGCGACCGCGAAAAATGCA
GGAGGTGGGGACGCACIITGCATCCAGACCTCCTCIGCATCGCAGTTCACGACATCCACGCIIGGGAAAG
ICCGIACCCGCGCCTGGAGCGCTIAAAGACACCCTGCCGCGGGICGGGCGAGGTGCAGCAGAAGTITCCC
GCGGIIGCAAAGTGCAGATGGCIGGACCGCAACAAAGTCTAGAGATGGGGTICGTIICTCAGAAAGACGC</code></pre>
<p>The first line in a FASTA file usually starts with a <code>&gt;</code> (greater-than) symbol. This first line is called the “description line”, and can contain descriptive information about the sequence in the subsequent lines. The description can be the ID or name of the sequence such as gene names. However, very infrequently you may see lines starting with a “;” (semicolon). These lines will be taken as a comment, and can hold additional descriptive information about the sequence in subsequent lines.</p>
</div>
<div id="fastq" class="section level3 hasAnchor" number="1.1.4">
<h3><span class="header-section-number">1.1.4</span> FASTQ<a href="data-transform.html#fastq" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.</p>
<p>A FASTQ file has four line-separated fields per sequence:</p>
<ol style="list-style-type: decimal">
<li>Field 1 begins with a ‘@’ character and is followed by a sequence identifier and an optional description (like a FASTA title line).</li>
<li>Field 2 is the raw sequence letters.</li>
<li>Field 3 begins with a ‘+’ character and is optionally followed by the same sequence identifier (and any description) again.</li>
<li>Field 4 encodes the quality values for the sequence in Field 2, and must contain the same number of symbols as letters in the sequence.</li>
</ol>
<p>A FASTQ file containing a single sequence might look like this:</p>
<pre><code>@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!&#39;&#39;*((((***+))%%%++)(%%%%).1***-+*&#39;&#39;))**55CCF&gt;&gt;&gt;&gt;&gt;&gt;CCCCCCC65</code></pre>
<p>Check <a href="https://en.wikipedia.org/wiki/FASTQ_format" class="uri">https://en.wikipedia.org/wiki/FASTQ_format</a> for more info.</p>
</div>
</div>
<div id="long-to-wide-matrix" class="section level2 hasAnchor" number="1.2">
<h2><span class="header-section-number">1.2</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27NA%3D%3D%27">Long To Wide Matrix</a><a href="data-transform.html#long-to-wide-matrix" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27NA%3D%3D%27">Long To Wide Matrix</a></p>
<p>In the demo1, paste three-column matrix including the expression of genes in different samples with long matrix format.</p>
<p>In the transforming parameters:</p>
<ul>
<li>Transform the column containing genes in long matrix to the row of wide matrix by selecting the option of <code>Gene</code> in the <code>Column used as rownames in wide format matrix</code> parameter;</li>
<li>Transform the column containing the value of samples in long matrix to the column of wide matrix by selecting the option of <code>Sample</code> in the <code>Column used as headers in wide format matrix</code> parameter;</li>
<li>Transform the column containing the expression of genes in long matrix to the value of wide matrix by selecting the option of <code>Expr</code> in the <code>Column used as numeric values</code> parameter;</li>
<li>Specify “0” to replace the missing value by inputting <code>0</code> in the textarea of <code>Specify to replace missing values</code> parameter;</li>
<li>Do not transfer all numbers to integer values by selecting <code>No</code> in the <code>Transfer all numbers to integer values</code> parameter;</li>
<li>Do not remove rows containing only zeros by selecting <code>No</code> in the <code>Remove rows containing only zeros</code> parameter.</li>
</ul>
</div>
<div id="merge-matrixes" class="section level2 hasAnchor" number="1.3">
<h2><span class="header-section-number">1.3</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27NQ%3D%3D%27">Merge matrixes</a><a href="data-transform.html#merge-matrixes" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27NQ%3D%3D%27">Merge matrixes</a></p>
<p>In the demo1, paste matrix1 including the expression of genes in different samples and matrix2 including the number of cells in different samples.</p>
<p>In the transforming parameters:</p>
<ul>
<li>Specify one column name in matrix1 as common column for merging by selecting the option of <code>ID</code> in the <code>Column used for merging in left matrix</code> parameter;</li>
<li>Specify one column name in matrix1 as common column for merging by selecting the option of <code>ID</code> in the <code>Column used for merging in right matrix</code> parameter;</li>
<li>Merge two matrixes common rows based on columns shared by the two matrixes by selecting the option of <code>inner</code> in the <code>Combined type</code> parameter.</li>
</ul>
</div>
<div id="wide-to-long-matrix" class="section level2 hasAnchor" number="1.4">
<h2><span class="header-section-number">1.4</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27OA%3D%3D%27">Wide To Long Matrix</a><a href="data-transform.html#wide-to-long-matrix" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27OA%3D%3D%27">Wide To Long Matrix</a></p>
<p>In the demo1, paste a matrix including the expression of genes in different samples with wide matrix format.</p>
<p>In the transforming parameters:</p>
<ul>
<li>Specify the names of column which would stay as original after transfer by selecting the option of <code>ID</code> in the <code>ID variable</code> parameter;</li>
<li>Specify “Expression” to be the column name in transferred long matrix to save all values by inputting <code>Expression</code> in the textarea of <code>Column name in long matrix to save all values</code> parameter;</li>
<li>Specify “Gene” to be the column name of all measured variables in transferred long matrix by inputting <code>Expression</code> in the textarea of <code>Column name in long matrix to save all values</code> parameter.</li>
</ul>
</div>
<div id="reverse-complement-sequences" class="section level2 hasAnchor" number="1.5">
<h2><span class="header-section-number">1.5</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjA%3D%27">Reverse Complement Sequences</a><a href="data-transform.html#reverse-complement-sequences" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjA%3D%27">Reverse Complement Sequences</a></p>
<p>In the demo1, paste a sequence with FASTA format.</p>
<p>In the transforming parameters:</p>
<ul>
<li>Specify the sequence is DNA sequence by selecting the option of <code>DNA</code> in the <code>Type of base sequences</code> parameter;</li>
<li>Specify output the reverse complementary sequences of the input sequences by selecting the option of <code>Reverse Complementary</code> in the <code>Operation type</code> parameter.</li>
</ul>
</div>
<div id="rna-translation" class="section level2 hasAnchor" number="1.6">
<h2><span class="header-section-number">1.6</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjQ%3D%27">RNA translation</a><a href="data-transform.html#rna-translation" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjQ%3D%27">RNA translation</a></p>
<p>In the demo1, paste a sequence with FASTA format.</p>
<p>In the transforming parameters:</p>
<ul>
<li>Specify translate sequences from the first frame by selecting the option of <code>the first frame</code> in the <code>Frames used for translation</code> parameter;</li>
<li>Specify translate sequences in positive strand by selecting the option of <code>Forward chain</code> in the <code>Select sequence strand</code> parameter;</li>
<li>Specify standard codon table by selecting the option of <code>Standard</code> in the <code>Codon table</code> parameter.</li>
</ul>
</div>
<div id="reverse-file-line" class="section level2 hasAnchor" number="1.7">
<h2><span class="header-section-number">1.7</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjY%3D%27">Reverse File Line</a><a href="data-transform.html#reverse-file-line" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p><a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjY%3D%27">Reverse File Line</a></p>
<p>In the demo1, paste a matrix including the expression of genes in different sample.</p>
<p>In the transforming parameters:</p>
<ul>
<li>Do not output the first line of the file in reverse by selecting the option of <code>True</code> in the <code>Header</code> parameter.</li>
</ul>

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